Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016123.1 Corchorus olitorius cultivar O-4 contig16156, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2898
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1154 original size:21 final size:21

Alignment explanation


    Indices: 1128--1182  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1118 CGGCCATTCA

                           **    
       1128 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       1149 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       1170 CCGTGCCATCACC
          1 CCGTGCCACCACC

       1183 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:1563 original size:15 final size:16

Alignment explanation


    Indices: 1535--1565  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1525 ATCCCTTTAA

                            
       1535 TTTTCCTTGCATTATT
          1 TTTTCCTTGCATTATT

                            
       1551 TTTTCCTTG-ATTATT
          1 TTTTCCTTGCATTATT

       1566 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    6  0.40
  16    9  0.60

ACGTcount: A:0.13, C:0.16, G:0.06, T:0.65


Consensus pattern (16 bp):   
TTTTCCTTGCATTATT

Found at i:1814 original size:54 final size:54

Alignment explanation


    Indices: 1732--1838  Score: 214
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1722 AGAGAGTCTA

                                                                  
       1732 GTCAATAGAGAGTCTGCATGCATCATAATCTTAAAATATACCATAATTTTTTCG
          1 GTCAATAGAGAGTCTGCATGCATCATAATCTTAAAATATACCATAATTTTTTCG

                                                                 
       1786 GTCAATAGAGAGTCTGCATGCATCATAATCTTAAAATATACCATAATTTTTTC
          1 GTCAATAGAGAGTCTGCATGCATCATAATCTTAAAATATACCATAATTTTTTC

       1839 AAAAATTTTG


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   53  1.00

ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36


Consensus pattern (54 bp):   
GTCAATAGAGAGTCTGCATGCATCATAATCTTAAAATATACCATAATTTTTTCG
Done.